estimatePsite {ribosomeProfilingQC} | R Documentation

## Estimate P site position

### Description

Estimate P site postion from a subset reads.

### Usage

    estimatePsite(bamfile, CDS, genome, anchor = "5end")

### Arguments

`bamfile` | A BamFile object.
`CDS` | Output of prepareCDS
`genome` | A BSgenome object.
`anchor` | 5end or 3end. Default is 5end.

### Value

A best P site position.

### References

1: Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. 2014 May 2;33(9):981-93. doi: 10.1002/embj.201488411. Epub 2014 Apr 4. PubMed PMID: 24705786; PubMed Central PMCID: PMC4193932.

### Examples

    library(Rsamtools)
    bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                               package="ribosomeProfilingQC")
    yieldSize <- 10000000
    bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
    #library(GenomicFeatures)
    library(BSgenome.Drerio.UCSC.danRer10)
    #txdb <- makeTxDbFromGFF(system.file("extdata",
     #         "Danio_rerio.GRCz10.91.chr1.gtf.gz",
     #         package="ribosomeProfilingQC"),
     #         organism = "Danio rerio",
     #         chrominfo = seqinfo(Drerio)["chr1"],
     #         taxonomyId = 7955)
    #CDS <- prepareCDS(txdb)
    CDS <- readRDS(system.file("extdata", "CDS.rds",
                               package="ribosomeProfilingQC"))
    estimatePsite(bamfile, CDS, Drerio)

[Package ribosomeProfilingQC version 0.99.9 Index]